Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1715242 original size:20 final size:20
Alignment explanation
Indices: 1715121--1715249 Score: 118
Period size: 20 Copynumber: 6.5 Consensus size: 20
1715111 ACAGGTTCTA
*
1715121 AAATTGCAACGCGAA-A-GT
1 AAATCGCAACGCGAATAGGT
* *
1715139 CAAATTCGCAACACGAATAGTT
1 -AAA-TCGCAACGCGAATAGGT
** *
1715161 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATAGGT
* *
1715181 AATTCGCAACGCAAATAGGT
1 AAATCGCAACGCGAATAGGT
** *
1715201 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATAGGT
*
1715221 AAATCACAACGCGAATAGGT
1 AAATCGCAACGCGAATAGGT
1715241 AAATCGCAA
1 AAATCGCAA
1715250 TGATAATATG
Statistics
Matches: 86, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
19 3 0.03
20 78 0.91
21 4 0.05
22 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATAGGT
Found at i:1715257 original size:20 final size:20
Alignment explanation
Indices: 1715154--1715264 Score: 125
Period size: 20 Copynumber: 5.5 Consensus size: 20
1715144 TCGCAACACG
*
1715154 AATAGTTAAATCGCAACGAT
1 AATAGGTAAATCGCAACGAT
* *
1715174 AATATGTAATTCGCAACGCA-
1 AATAGGTAAATCGCAACG-AT
1715194 AATAGGTAAATCGCAACGAT
1 AATAGGTAAATCGCAACGAT
* * **
1715214 AATATGTAAATCACAACGCG
1 AATAGGTAAATCGCAACGAT
*
1715234 AATAGGTAAATCGCAATGAT
1 AATAGGTAAATCGCAACGAT
*
1715254 AATATGTAAAT
1 AATAGGTAAAT
1715265 TACAACGTAA
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.01
20 72 0.97
21 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.24
Consensus pattern (20 bp):
AATAGGTAAATCGCAACGAT
Found at i:1715263 original size:40 final size:40
Alignment explanation
Indices: 1715147--1715271 Score: 187
Period size: 40 Copynumber: 3.1 Consensus size: 40
1715137 GTCAAATTCG
* * * *
1715147 CAACACGAATAGTTAAATCGCAACGATAATATGTAATTCG
1 CAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCA
*
1715187 CAACGCAAATAGGTAAATCGCAACGATAATATGTAAATCA
1 CAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCA
* *
1715227 CAACGCGAATAGGTAAATCGCAATGATAATATGTAAATTA
1 CAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCA
1715267 CAACG
1 CAACG
1715272 TAAATTCTCC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (40 bp):
CAACGCGAATAGGTAAATCGCAACGATAATATGTAAATCA
Found at i:1715546 original size:20 final size:20
Alignment explanation
Indices: 1715497--1715558 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1715487 GTTAAATTGT
*
1715497 AACGATAATATGTAATTCAC
1 AACGATAATATGTAAATCAC
* *
1715517 AAC-ACGAATAGGTAAATCAC
1 AACGA-TAATATGTAAATCAC
1715537 AACGATAATATGTAAATCAC
1 AACGATAATATGTAAATCAC
1715557 AA
1 AA
1715559 TGCGAATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (20 bp):
AACGATAATATGTAAATCAC
Found at i:1715565 original size:40 final size:40
Alignment explanation
Indices: 1715470--1715565 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
1715460 GCGAAAGTTA
* * ***
1715470 AAATCGCAACGCGAATAGTTAAATTGTAACGATAATATGT
1 AAATCACAACGCGAATAGGTAAATCACAACGATAATATGT
* *
1715510 AATTCACAACACGAATAGGTAAATCACAACGATAATATGT
1 AAATCACAACGCGAATAGGTAAATCACAACGATAATATGT
*
1715550 AAATCACAATGCGAAT
1 AAATCACAACGCGAAT
1715566 TCTCCAATTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.24
Consensus pattern (40 bp):
AAATCACAACGCGAATAGGTAAATCACAACGATAATATGT
Found at i:1715711 original size:20 final size:20
Alignment explanation
Indices: 1715686--1715737 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
1715676 TTTTCCAAAT
1715686 TCGCAACGCGAATAGGTAAA
1 TCGCAACGCGAATAGGTAAA
** * *
1715706 TCGCAACGATAATATGTTAA
1 TCGCAACGCGAATAGGTAAA
*
1715726 TCGCAACACGAA
1 TCGCAACGCGAA
1715738 ATCTCCAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAGGTAAA
Found at i:1726542 original size:2 final size:2
Alignment explanation
Indices: 1726535--1726564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1726525 CTTTTTATTA
1726535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1726565 TGTGTGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1731547 original size:12 final size:12
Alignment explanation
Indices: 1731530--1731557 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1731520 AATTTTAAAA
1731530 AAAATAATTATT
1 AAAATAATTATT
1731542 AAAATAATTATT
1 AAAATAATTATT
1731554 AAAA
1 AAAA
1731558 CATAATTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATAATTATT
Found at i:1732006 original size:21 final size:20
Alignment explanation
Indices: 1731982--1732025 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1731972 TTAAATGTTT
1731982 TTAATTCAAAAAAAATTATAA
1 TTAATTCAAAAAAAA-TATAA
* * *
1732003 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAAAATATAA
1732023 TTA
1 TTA
1732026 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTCAAAAAAAATATAA
Found at i:1732205 original size:184 final size:183
Alignment explanation
Indices: 1731979--1732347 Score: 600
Period size: 184 Copynumber: 2.0 Consensus size: 183
1731969 AAATTAAATG
*
1731979 TTTTTAATTCAAAAAAAATTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
1 TTTTTAATTCAAAAAAAATTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
1732044 TAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTA-TTGAATCTTAAATTATTAATT
66 TAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTTG-ATCTTAAATTATTAATT
* * *
1732108 GGGTTTTAAATGGTTTGGGCTT-ATCCCATAAGTTATATATAATATATTTAATAT
130 GAGTTTTAAATGGTTTGGG-TTAAGCCAATAAGTTATATATAATATATTTAATAT
* *
1732162 TTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
1 TTTTTAATTCAAAAAA-A-ATTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCA
* *
1732226 TATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTTGATCTTAAATTATTAAT
64 GATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTTGATCTTAAATTATTAAT
*
1732291 TGAGTTTTAAATGGTTTGGGTTAAGCCAATATGTTATATATAATATATTTAATAT
129 TGAGTTTTAAATGGTTTGGGTTAAGCCAATAAGTTATATATAATATATTTAATAT
1732346 TT
1 TT
1732348 AAATTTTAAT
Statistics
Matches: 173, Mismatches: 9, Indels: 7
0.92 0.05 0.04
Matches are distributed among these distances:
182 6 0.03
183 12 0.07
184 152 0.88
185 3 0.02
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (183 bp):
TTTTTAATTCAAAAAAAATTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAGA
TAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTTGATCTTAAATTATTAATTG
AGTTTTAAATGGTTTGGGTTAAGCCAATAAGTTATATATAATATATTTAATAT
Found at i:1735109 original size:21 final size:22
Alignment explanation
Indices: 1735083--1735132 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
1735073 CCGGTCACTC
1735083 AATTTTTTAAACCCCAAACC-G
1 AATTTTTTAAACCCCAAACCAG
*
1735104 AA-TTTTTAAACCCCAGACCAG
1 AATTTTTTAAACCCCAAACCAG
*
1735125 ATTTTTTT
1 AATTTTTT
1735133 CCGGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.64
21 4 0.16
22 5 0.20
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (22 bp):
AATTTTTTAAACCCCAAACCAG
Found at i:1743039 original size:16 final size:17
Alignment explanation
Indices: 1743005--1743037 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1742995 CTCTACATGT
1743005 ATAATTAATTTTACTAA
1 ATAATTAATTTTACTAA
1743022 ATAATT-ATTTTA-TAA
1 ATAATTAATTTTACTAA
1743037 A
1 A
1743038 ATTGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTAATTTTACTAA
Found at i:1745611 original size:31 final size:31
Alignment explanation
Indices: 1745576--1745669 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
1745566 AAAAACCAAG
*
1745576 TTCAAATTTTGGTTTGGTCCCTTCATAATGC
1 TTCAAATTTTGATTTGGTCCCTTCATAATGC
* * *
1745607 TTC-AATTTAGAATTTAGT--CTATC-CAA-G-
1 TTCAAATTTTG-ATTTGGTCCCT-TCATAATGC
*
1745634 TTCAAATTTTGTTTTGGTCCCTTCATAATGC
1 TTCAAATTTTGATTTGGTCCCTTCATAATGC
1745665 TTCAA
1 TTCAA
1745670 TTTAGAATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 8 0.17
28 9 0.19
29 8 0.17
30 9 0.19
31 13 0.28
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.45
Consensus pattern (31 bp):
TTCAAATTTTGATTTGGTCCCTTCATAATGC
Found at i:1745641 original size:58 final size:58
Alignment explanation
Indices: 1745571--1745686 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
1745561 GAATAAAAAA
1745571 CCAAGTTCAAATTTTGGTTTGGTCCCTTCATAATGCTTCAATTTAGAATTTAGTCTAT
1 CCAAGTTCAAATTTTGGTTTGGTCCCTTCATAATGCTTCAATTTAGAATTTAGTCTAT
*
1745629 CCAAGTTCAAATTTTGTTTTGGTCCCTTCATAATGCTTCAATTTAGAATTTAGTCTAT
1 CCAAGTTCAAATTTTGGTTTGGTCCCTTCATAATGCTTCAATTTAGAATTTAGTCTAT
1745687 ATAGTTTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (58 bp):
CCAAGTTCAAATTTTGGTTTGGTCCCTTCATAATGCTTCAATTTAGAATTTAGTCTAT
Found at i:1746063 original size:2 final size:2
Alignment explanation
Indices: 1746056--1746115 Score: 52
Period size: 2 Copynumber: 31.0 Consensus size: 2
1746046 TTAAAACAAA
* * * * *
1746056 AT AT AT AT A- AT AT AT AA AA AC AA AT AT AT AT A- AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1746096 AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1746116 TTCGAAAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1746073 original size:23 final size:23
Alignment explanation
Indices: 1746048--1746093 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1746038 TGTTTTGGTT
1746048 AAAACAAAATATATATAATATATA
1 AAAAC-AAATATATATAATATATA
1746072 AAAACAAATATATATAATATAT
1 AAAACAAATATATATAATATAT
1746094 CTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAACAAATATATATAATATATA
Found at i:1759470 original size:16 final size:16
Alignment explanation
Indices: 1759449--1759503 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1759439 CATTTAATAA
*
1759449 ATAAACGAACATGAAC
1 ATAAACGAACACGAAC
*
1759465 ATAAACGAACACGAGC
1 ATAAACGAACACGAAC
**
1759481 ATAAATAAACACGAAC
1 ATAAACGAACACGAAC
*
1759497 ACAAACG
1 ATAAACG
1759504 TTGGAGACCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:1761789 original size:29 final size:30
Alignment explanation
Indices: 1761739--1761812 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
1761729 CTATAGTCAA
** * *
1761739 AAATCAATGTGACTACCGAACT-TTCAATT
1 AAATCAATCAGACCACCCAACTATTCAATT
*
1761768 AAATCAATCAGACCACCCAACTATTTAATT
1 AAATCAATCAGACCACCCAACTATTCAATT
* *
1761798 GAATTAATCAGACCA
1 AAATCAATCAGACCA
1761813 TCGACCGTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATCAATCAGACCACCCAACTATTCAATT
Found at i:1762152 original size:23 final size:23
Alignment explanation
Indices: 1762122--1762165 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1762112 TGATTAGATA
*
1762122 AAAAAATT-ATTAAATTAAATAAT
1 AAAAAATTCA-TAAATAAAATAAT
1762145 AAAAAATTCATAAATAAAATA
1 AAAAAATTCATAAATAAAATA
1762166 TTCCAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAAATTCATAAATAAAATAAT
Found at i:1762406 original size:29 final size:30
Alignment explanation
Indices: 1762348--1762409 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1762338 GGTATGATTG
**
1762348 ATTCAATTAAATAGTTGGATGGTCTGATTA
1 ATTCAATTAAATAGTTGGATGGTCACATTA
*
1762378 ATTCAATTGAA-AGTTCGG-TGGTCACATTA
1 ATTCAATTAAATAGTT-GGATGGTCACATTA
1762407 ATT
1 ATT
1762410 TTTGACCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 16 0.57
30 12 0.43
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (30 bp):
ATTCAATTAAATAGTTGGATGGTCACATTA
Found at i:1762617 original size:21 final size:21
Alignment explanation
Indices: 1762588--1762628 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1762578 TTTTAAAATG
*
1762588 TTTTT-AAAATTATTTTTTAT
1 TTTTTAAAAATAATTTTTTAT
1762608 TTTTTAAAAAATAATTTTTTA
1 TTTTT-AAAAATAATTTTTTA
1762629 AAAACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTAAAAATAATTTTTTAT
Done.